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Trim Galore. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/"},{"key":"10.1016\/j.cell.2026.06.022_bib75","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cell.2026.06.022_bib96","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/978-1-4939-0512-6_4","article-title":"Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells","volume":"1150","author":"Liu","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.cell.2026.06.022_bib76","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2026.06.022_bib77","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.cell.2026.06.022_bib78","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with Signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cell.2026.06.022_bib79","unstructured":"Korsunsky, I., M.H., Patikas, N., Yao, H., Millard, N., Fan, J., Slowikowski, K., and Raychaudhuri, S. (2023). harmony: Fast, Sensitive, and Accurate Integration of Single Cell Data. https:\/\/CRAN.R-project.org\/package=harmony. CRAN."},{"key":"10.1016\/j.cell.2026.06.022_bib80","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-27729-z","article-title":"Zero-preserving imputation of single-cell RNA-seq data","volume":"13","author":"Linderman","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2026.06.022_bib81","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1016\/j.csbj.2021.06.043","article-title":"UCell: Robust and scalable single-cell gene signature scoring","volume":"19","author":"Andreatta","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.cell.2026.06.022_bib82","article-title":"Fast gene set enrichment analysis","author":"Korotkevich","year":"2019","journal-title":"bioRxiv"},{"key":"10.1016\/j.cell.2026.06.022_bib83","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb.)"},{"key":"10.1016\/j.cell.2026.06.022_bib84","author":"Amezquita"},{"key":"10.1016\/j.cell.2026.06.022_bib85","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.cell.2026.06.022_bib86","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/nature10730","article-title":"Differential oestrogen receptor binding is associated with clinical outcome in breast cancer","volume":"481","author":"Ross-Innes","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.cell.2026.06.022_bib87","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.1093\/bioinformatics\/btv145","article-title":"ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.06.022_bib88","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cell.2026.06.022_bib89","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.06.022_bib90","author":"Carroll"},{"key":"10.1016\/j.cell.2026.06.022_bib91","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cell.2026.06.022_bib92","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat. 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